Unable to escape \$ for nix

gatk.nix

{ stdenv, fetchFromGitHub, jdk, maven, jre, makeWrapper, ... }:

let
  
  mavenDependenciesSha256 = "0cfj312zcf33s89qxpqycc3j8cnz44svylzxjg94d5147a5ddazb";

  src = fetchFromGitHub {
    owner = "broadgsa";
    repo = "gatk-protected";
    sha256 = "025v8wxqnp3bab2g5pblrrd2yiy7w1jw7nd09544wamf8in8a8v6";
    rev = "aa8764d6c3de146856b174a8674fa787a6311d7c";
  };

  # This is adapted from https://github.com/volth/nixpkgs/blob/6aa470dfd57cae46758b62010a93c5ff115215d7/pkgs/applications/networking/cluster/hadoop/default.nix#L20-L32
  fetchedMavenDeps = stdenv.mkDerivation rec {
    
    inherit src mavenDependenciesSha256;
   
    buildInputs = [ maven ];

    version = "3.8-1"; 

    name = "gatk3-${version}-maven-deps";

    patchPhase = ''
      substituteInPlace ./public/src/main/scripts/shell/delete_maven_links.sh \
        --replace "#!/bin/bash" "#!/usr/bin/env bash"

      substituteInPlace ./public/src/main/scripts/shell/check_utils_engine_tools.sh \
        --replace "#!/bin/sh" "#!/usr/bin/env sh"
      
      substituteInPlace pom.xml \
        --replace "\${gatk.shell.directory}/check_utils_engine_tools.sh" "./public/src/main/scripts/shell/check_utils_engine_tools.sh"
    '';
    
    buildPhase = ''
      mvn -Dmaven.repo.local=$out/.m2 dependency:resolve-plugins
      while timeout --kill-after=21m 20m mvn package -Dmaven.repo.local=$out/.m2; [ $? = 124 ]; do
        echo "maven hangs while downloading :("
      done
      echo "FINISHED BUILDING, DID WE GET MORE THAN JUST DEPS?"
      ls -hal .
      ls -hal ./public
    '';
    
    installPhase = ''
      find $out/.m2 -type f \! -regex '.+\(pom\|jar\|xml\|sha1\)' -delete
    ''; # delete files with lastModified timestamps inside
    
    outputHashAlgo = "sha256";
    outputHashMode = "recursive";
    outputHash =  mavenDependenciesSha256;

  };
in
stdenv.mkDerivation rec {
  
  name = "gatk3";

  version = "3.8-1";

  inherit src;

  buildInputs = [ makeWrapper jdk maven ];

  buildPhase = ''
    mvn package --offline -Dmaven.repo.local=$(cp -dpR ${fetchedMavenDeps}/.m2 ./ && chmod +w -R .m2 && pwd)/.m2
  '';

  installPhase = ''
      mkdir -p $out/bin
      cp target/GenomeAnalysisTK.jar $out/bin/GenomeAnalysisTK.jar
      makeWrapper ${jre}/bin/java $out/bin/GenomeAnalysisTK.jar --add-flags "-jar"
  '';

}